getInfo: IFC File Information Extraction

In IFC: Tools for Imaging Flow Cytometry

IFC File Information Extraction

Description

Retrieves rich information from RIF, CIF and DAF files.

Usage

getInfo(
  fileName,
  from = c("acquisition", "analysis")[2],
  verbose = FALSE,
  verbosity = 1,
  warn = TRUE,
  force_default = TRUE,
  cifdir = dirname(fileName),
  ntry = +Inf,
  ...
)

Arguments

fileName	path to file..
from	whether to extract information from 'acquisition' or 'analysis'. Default is 'analysis'.
verbose	whether to display information (use for debugging purpose). Default is FALSE.
verbosity	quantity of information print to console when verbose is TRUE; 1: normal, 2: rich. Default is 1.
warn	whether to send warning message when trying to read 'analysis' information from a 'rif' file. Default is TRUE.
force_default	when display information can't be retrieved whether to use default values. Default is TRUE.
cifdir	the path of the directory to initially look to cif file. Default is dirname(fileName). Only apply when 'fileName' is a .daf file.
ntry	number of times getInfo will be allowed to find corresponding cif file. Default is +Inf. Only apply when 'fileName' is a .daf file. If cif can't be found, but 'ntry' is reached, then an error will be thrown.
...	other arguments to be passed.

Value

a list of information (open .daf file in an text editor for more details) about input fileName of class 'IFC_info' and 'acquistion' or 'analysis', whose members are:
-objcount, number of object in file,
-date, date of file creation,
-instrument, instrument identification,
-sw_raw, version of software for raw data,
-sw_processed, version of software for processed data,
-channelwidth, default channel width in pixel,
-in_use, channels used,
-brightfield, whether brightfield is applied on channels and its intensity,
-illumination, laser illumination parameters,
-collectionmode, the collection mode,
-magnification, magnification used,
-coremode, the core mode,
-evmode, the high gain mode,
-CrossTalkMatrix. compensation matrix applied,
-ChannelPresets, channel preset,
-ImageDisplaySettings, image display settings,
-Images, information about colors, range and channels,
-masks, masks defined,
-ViewingModes, modes of visualization,
-checksum, checksum computed,
-Merged_rif, character vector of path of files used to create rif, if input file was a merged,
-Merged_cif, character vector of path of files used to create cif, if input file was a merged,
-XIF_test, integer defining XIF type,
-checksum, integer corresponding to file checksum,
-fileName, path of fileName input,
-fileName_image, path of fileName_image.

Examples

if(requireNamespace("IFCdata", quietly = TRUE)) {
  ## use a daf file
  file_daf <- system.file("extdata", "example.daf", package = "IFCdata")
  info <- getInfo(fileName = file_daf, from = "analysis")
  ## show some information
  print(info$Images)
} else {
  message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
                  'https://gitdemont.github.io/IFCdata/',
                  'to install extra files required to run this example.'))
}

IFC documentation built on Sept. 14, 2023, 1:08 a.m.